Wow, I have so many pent up feelings on this topic that I don't know where to start. To start with badger's original question: You got the shift rotation right, but it is closer to 9 hours per day than 8. Don't forget the extra time for additional or advanced qualification exams (which somehow never occur on your shift), critiques, extra-early before shift briefings during shutdown or testing periods, and STUDENTS. When I was a Shift Supervisor at prototype I was amazed by how much extra time my crew would put in to get their guys (and gals) qualified on time.
Your time to qualify depends on what you are qualifying (MO=EO=RO is around 14 weeks (?? help), then you get another 2 weeks or so for ELT, +time for EWS, +time for EOOW). I can't remember the rules, but it sounds like you will not meet the wickets for initial EWS or EOOW quals, so don't worry about it. You also get some extra time based on when you attend Prospective Staff Instructor class during your quals. As ddklbl pointed out, one of the FEW benefits for enlisted staff duty at prototype is the ability to qualify EOOW. If you want to do that: let everyone know, and do your assigned jobs as well as you can. That subject can get really long, if you want to talk about it, send me a PM.
Being a sub or surface sailor should not affect your possibilities at prototype. You will find people in your chain of command with prejudices, but if you are a good staff instructor, no one will care. [Case in point, I had an ET1/SS who was qualified EWS on his boat and at prototype. He was the only ET1 in my RC-Div, so the Operations Officer ordered me to make him the RC-Div Section LPO. He was a soup sandwich. He stood waterbrake over checkout cube every day. The best two RO watchstanders in my crew were staff pickups. One was qualified 6 mos, the other 9. I had to go through an NPEB ORSE with those two SPUs on the panel. Bless them both, they were good nukes.]
That rambling story leads me to the SPU vs. sea returnee discussion. Sea returnees are not treated "better" than SPUs, they are just given more responsibility and expected to perform better. Sea returnees are treated with more respect because of their experience and qualifications, but also given less slack.
Finally, I unfortunately have to agree with your decision to avoid NPTU Ballston Spa. I have seen the sad state of affairs there. I am afraid that the government is micromanaging that place right into the toilet. It is unfortunate because I believe that the KSO model of civilian and Navy cooperation is inherently better than the organizational structure at MTS. I can debate that if anyone is interested...

Good luck with your decision. As my favorite Leading Crew Chief once told me, "The only place worse than prototype is the shipyard during overhaul."
